Mark G Thomas

University College London | UCL · Department of Genetics, Evolution and Environment (GEE)

The rise of zoonotic diseases in prehistory is often associated with the Neolithic agricultural transition. In particular, plague has been linked to population declines in Late Neolithic Europe. Although plague is amongst the most devastating diseases in human history, early strains of Yersinia pestis, the causal agent of plague, lack virulence fac...

This article presents a series of recommendations for the publication of archaeological data, to improve their usability. These 12 recommendations were formulated by archaeological data experts who mined thousands of publications for different data types (including funerary practices, accelerator mass spectrometry dating, stable isotopes, zooarchae...

Zooarchaeological age-at-death profiles for domesticated ruminants can be inferred from tooth eruption, replacement and wear. These profiles contain important information on slaughter management, and have been used informally to infer the goals of past husbandry strategies. In principle, sex-specific survival curves could inform on various producti...

Big Data are currently having a profound impact on archaeological research. Traditional methodologies allow deep but arguably narrow interpretations. Quantitative computational analysis of Big Data combines traditional close reading of data with a sweeping 'bird's-eye' approach that can reveal hitherto unrecognised broader patterns and trends and p...

The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration as it connected the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7,000 BCE to 1,800 CE to study migration and mobility history in the region, with a particular focus on historic...

The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples. We present genome-wide ancient DNA data for 181 individuals from this region spanning the Mesolithic, Neolithic and Bronze Age. We find that Early to Mid-Holocene hunter-gatherer populations from across the southern forest...

In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The ev...

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Background/Objectives: High-throughput sequencing has profoundly increased the availability of genetic markers in the non-recombinant region of the Y-chromosome (NRY) and has prompted the development of haplogroup classification tools. Here we compared five tools for human NRY haplogroup classification. In addition, the most accurate tool was used...

Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republ...

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture¹. The extent to which migration from continental Europe mediated these transitions is a matt...

The non-recombinant region of the Y chromosome (NRY) contains a great number of polymorphic markers that allows to accurately reconstruct pedigree relationships and retrieve ancestral information from study samples. The analysis of NRY is typically implemented in anthropological, medical, and forensic studies. High-throughput sequencing (HTS) has p...

We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closel...

In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configu...

Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age¹. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between...

We present 100 new complete mitogenomes from a population sample of Cameroonian individuals, which contribute to the currently underrepresented African mitochondrial DNA sequence archive. Cameroon is considered an “Africa in miniature” due to its high ecological, genetic, linguistic, and ethnic diversity. The majority of sequences belong to the mai...

The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with–and shape–genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with informatio...

Attempts to identify a ‘homeland’ for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a ‘homeland’ is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variat...

Large anthropogenic ¹⁴ C datasets are widely used to generate summed probability distributions (SPDs) as a proxy for past human population levels. However, SPDs are a poor proxy when datasets are small, bearing little relationship to true population dynamics. Instead, more robust inferences can be achieved by directly modelling the population and a...

Lactase persistence (LP), the continued expression of lactase into adulthood, is the most strongly selected single gene trait over the last 10,000 years in multiple human populations. It has been posited that the primary allele causing LP among Eurasians, rs4988235-A [1], only rose to appreciable frequencies during the Bronze and Iron Ages [2, 3],...

1. Biologists often seek to geographically provenance organisms using their traits. This is typically achieved by defining spatial groups using distinct patterns of trait variation. 2. Here we present a new spatial provenancing and trait boundary identification methodology based on correlations between geographic and trait distances, which requir...

Cancer risk is highly variable in carriers of the common TP53-R337H founder allele, possibly due to the influence of modifier genes. Whole-genome sequencing identified a variant in the tumor suppressor XAF1 (E134*/Glu134Ter/ rs146752602) in a subset of R337H carriers. Haplotype-defining variants were verified in 203 patients with cancer, 582 relati...

https://www.nature.com/articles/d41586-020-01080-7

Analysis of ancient human DNA from western Central Africa offers insights into African population history, including the origin of speakers of the Bantu languages. The findings are reported in this week’s Nature. Shum Laka in western Cameroon, Africa, is an important archaeological site for the study of Late Pleistocene and Holocene prehistory in...

Chan and colleagues in their paper titled “Human origins in a southern African palaeo-wetland and first migrations” (https://www.nature.com/articles/s41586-019-1714-1) report 198 novel whole mitochondrial DNA (mtDNA) sequences and infer that ‘anatomically modern humans’ originated in the Makgadikgadi–Okavango palaeo-wetland of southern Africa aroun...

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world’s most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700...

Aveline's Hole is the largest known Early Mesolithic cemetery in Britain, previously thought to have no evidence for subsequent burial activity. Thus, it came as some surprise when the results of a recent ancient human DNA study found that, of four individuals from the site yielding genomic data, two showed high levels of ancestry from Early Neolit...

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. Genetic data are consistent with a diverse and subdivided African ancestry, potentially including gene flow with currently unidentified African archaic populations. The chronology and physical diversity of Pleistocene human fossils also...

The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure in human populations. Using primarily novel genetic variation data covering 1,268 Ethiopians representing 68 different ethnic groups, together with in...

The past half century has seen a move from a multiregionalist view of human origins to widespread acceptance that modern humans emerged in Africa. Here the authors argue that a simple out-of-Africa model is also outdated, and that the current state of the evidence favours a structured African metapopulation model of human origins.

Humans expanded out of Africa 50,000-70,000 years ago, but many details of this migration are poorly understood. Here, Haber et al. sequence Y chromosomes belonging to a rare African lineage and analyze... Present-day humans outside Africa descend mainly from a single expansion out ∼50,000–70,000 years ago, but many details of this expansion remain...

CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retain...

In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa...

In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200–400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC–50 AD) (EstIA). We also includ...

On the evolutionary timescale, milk and milk products are relatively recent additions to adult human diets that have had profound impacts on our culture, biology, genetics, and behaviour. All mammals produce milk to feed their offspring, with lactose as the principal carbohydrate. Humans, however, are one of the few species to incorporate milk and...

Milk and dairy food consumption can lead to a range of adverse clinical symptoms, the best known of which is lactose intolerance (LI). LI is defined as experiencing gastrointestinal symptoms following the ingestion of lactose. While LI is often caused by a genetically determined reduction of lactase production in adulthood, it is important to note...

Forager mobility tends to be high, although ethnographic studies indicate ecological factors such as resource abundance and reliability, population density and effective temperature influence the cost-to-benefit assessment of movement decisions. We investigate the evolution of mobility using an agent-based and spatially explicit cultural evolutiona...

Significance State centralization occurs when previously separate communities are united, forming a single political system often associated with economy, trade, warfare, and culture. One example is the precolonial Kuba Kingdom of the Democratic Republic of the Congo (DRC). Using genetic data from over 690 individuals from the DRC, we compared indi...

The prevailing explanation for Neanderthal body form is the cold (glacial) adaptation hypothesis. However, palaeoecological associations appear to indicate a less cold woodland environment. Under such conditions, encounter and ambush (rather than pursuit) hunting-and thus muscular power and sprint (rather than endurance) capacity-would have been fa...

Table_S1_Chinese_Panicum_samples_and_genotypes_050218 – Supplemental material for Genetic evidence for a western Chinese origin of broomcorn millet (Panicum miliaceum)

This contribution describes the discovery and subsequent investigation of a cist in a rock-cut pit at Achavanich, Highland. Discovered and excavated in 1987, the cist was found to contain the tightly contracted skeletal remains of a young woman, accompanied by a Beaker, three flint artefacts and a cattle scapula. Initial post excavation work establ...

Direct-to-consumer genetic ancestry testing is a new and growing industry that has gained widespread media coverage and public interest. Its scientific base is in the fields of population and evolutionary genetics and it has benefitted considerably from recent advances in rapid and cost-effective DNA typing technologies. There is a considerable bod...

Age-at-death profiles constructed from archaeozoological data have been used for decades to infer the goals of prehistoric herd management strategies. Several 'ideal' profiles have been proposed as models for the optimal kill-off profiles that represent specific husbandry strategies, such as maximising milk or meat yields, which can then be compare...

Broomcorn millet (Panicum miliaceum) is a key domesticated cereal that has been associated with the north China centre of agricultural origins. Early archaeobotanical evidence for this crop has generated two major debates. First, its contested presence in pre-7000 cal. BP sites in eastern Europe has admitted the possibility of a western origin. Sec...

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the...

Important nutritional resources can be acquired by breaking bone shafts to access marrow, whereas heavy comminution and boiling of cancellous bone is required to extract bone grease. Since labour and fuel costs of these processes differ considerably, the relative intensities of these activities provide a possible proxy for nutritional stress or ele...

CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retain...

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and t...

This corrects the article DOI: 10.1038/nature25738.

From around 2750 to 2500 BC, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 BC. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide...

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Anatolian ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers 1–9 . Neolithic cultures first appear in Brita...

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and tha...

Liddle syndrome is considered a rare Mendelian hypertension. We have previously described 3 reportedly unrelated families, native of an Italian area around the Strait of Messina, carrying the same mutation (βP617L) of the epithelial sodium channel. The aims of our study were (1) to evaluate whether a close genomic relationship exists between the 3...

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the post-introgression population dynamics of these putative cases of adaptive introgression. Here, for th...

The genetic trait of lactase persistence (LP) is associated with at least five independent functional single nucleotide variants in a regulatory region about 14 kb upstream of the lactase gene [−13910*T (rs4988235), −13907*G (rs41525747), −13915*G (rs41380347), −14009*G (rs869051967) and −14010*C (rs145946881)]. These alleles have been inferred to...

Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for...

Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are p...